Biotechnological potential of the ethylmalonyl-CoA pathway

Applied Microbiology and Biotechnology

Volumn 89, Issue 1, 2011, Pages 17-25

  Alber, Birgit E ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

2 Methylfumaryl CoA; Claisen condensation; Crotonyl CoA carboxylase reductase; Ethylmalonyl CoA pathway; Glyoxylate cycle; Thioesterase

Indexed keywords

2-METHYLFUMARYL-COA; CLAISEN CONDENSATION; CROTONYL-COA CARBOXYLASE/REDUCTASE; ETHYLMALONYL-COA PATHWAY; GLYOXYLATE; THIOESTERASES;

BIOCHEMISTRY; BIOTECHNOLOGY; CARBOXYLATION; CONDENSATION; ENZYMES; ESTERS; METABOLISM;

CATALYSTS;

ACETYL COENZYME A; ACYL COENZYME A; CARBOXYLASE; CROTONYL COENZYME A; ETHYLMALONYL COENZYME; GLYOXYLIC ACID; MALATE SYNTHASE; MESACONYL COENZYME A; METHYLMALYL COENZYME A; METHYLSUCCINYL COENZYME A; OXIDOREDUCTASE; THIOL ESTER HYDROLASE; UNCLASSIFIED DRUG;

BACTERIUM; BIOTECHNOLOGY; CATALYST; ENZYME ACTIVITY; METABOLISM; METABOLITE;

ARTICLE; BIOTECHNOLOGICAL PROCEDURES; CARBON METABOLISM; CARBOXYLATION; CATALYST; CLAISEN CONDENSATION; METHYLOBACTERIUM EXTORQUENS; NONHUMAN; RHODOBACTER SPHAEROIDES; SIGNAL TRANSDUCTION; STREPTOMYCES;

ACYL COENZYME A; BACTERIA; BACTERIAL PROTEINS; BIOSYNTHETIC PATHWAYS; CARBON; INDUSTRIAL MICROBIOLOGY;

ACTINOBACTERIA (CLASS); ALPHAPROTEOBACTERIA; METHYLOBACTERIUM EXTORQUENS; RHODOBACTER SPHAEROIDES; STREPTOMYCES;

EID: 78651104413     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-010-2873-z     Document Type: Article

References (71)

1. BE Alber R Spanheimer C Ebenau-Jehle G Fuchs 2006 Study of an alternate glyoxylate cycle for acetate assimilation by Rhodobacter sphaeroides Mol Microbiol 61 297 309 1:CAS:528:DC%2BD28XotVeqtr0%3D 10.1111/j.1365-2958.2006. 05238.x (Pubitemid 44356564)
2. Anthony C (1982) The biochemistry of methylotrophs. Academic, London
3. H Arai JH Roh S Kaplan 2008 Transriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration in Rhodobacter sphaeroides 2.4.1 J Bacteriol 190 286 299 1:CAS:528:DC%2BD1cXhsF2rsg%3D%3D 10.1128/JB.01375-07
4. EM Barnes SJ Wakil 1968 Studies of the mechanism of fatty acid synthesis. XIX. Preparation and general properties of palmityl thioesterase J Biol Chem 243 2955 2962 1:CAS:528:DyaF1cXktVShtr8%3D
5. CE Bauer TH Bird 1996 Regulatory circuits controlling photosynthesis gene expression Cell 85 5 8 1:CAS:528:DyaK28Xit1aksLg%3D 10.1016/S0092-8674(00) 81074-0 (Pubitemid 26116801)
6. MM Benning G Wesenberg R Liu KL Taylor D Dunaway-Mariano HM Holden 1998 The three-dimensional structure of 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. strain CBS-3 J Biol Chem 273 33572 33579 1:CAS:528: DyaK1MXovA%3D%3D 10.1074/jbc.273.50.33572 (Pubitemid 29005743)
7. CL Berthold CG Toyota NGJ Richards Y Lindqvist 2008 Reinvestigation of the catalytic mechanism of formyl-CoA transferase, a class III CoA-transferase J Biol Chem 283 6519 6529 1:CAS:528:DC%2BD1cXisFOkt78%3D 10.1074/jbc.M709353200
8. W Buckel U Dorn R Semmler 1981 Glutaconate CoA-transferase from Acidaminococcus fermentas Eur J Biochem 118 315 321 1:CAS:528:DyaL3MXlt1yjt7w%3D 10.1111/j.1432-1033.1981.tb06404.x
9. 12 dependent mutases Chem Eur J 12 352 362 10.1002/chem.200501074 (Pubitemid 43019232)
10. J Cao X Hang H Zhao W Gong D Dunaway-Mariano 2009 The mechanism of human hotdog-fold thioesterase 2 (hTHEM2) substarte recognition and catalysis illuminated by a structure and function based analysis Biochemistry 48 1293 1304 1:CAS:528:DC%2BD1MXhtVaqurc%3D 10.1021/bi801879z
11. YA Chan AM Podevels BM Kevany MG Thomas 2009 Biosynthesis of polyketide synthase extender units Nat Prod Rep 26 10 114 10.1039/b801658p
12. L Chisterodova MG Kalyuzhnaya ME Lidstrom 2009 The expanding world of methylotrophic metabolism Annu Rev Microbiol 63 477 499 10.1146/annurev.micro. 091208.073600
13. L Chistoserdova ME Lidstrom 1996 Molecular characterization of a chromosomal region involved in the oxidation of acetyl-CoA to glyoxylate in the isocitrate-lyase-negative methylotroph Methylobacterium extorquens AM1 Microbiology 142 1459 1468 10.1099/13500872-142-6-1459
14. L Chistoserdova S-W Chen A Lapidus ME Lidstrom 2003 Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view J Bacteriol 185 2980 2987 1:CAS:528:DC%2BD3sXjs1aqu7s%3D 10.1128/JB.185.10.2980-2987.2003 (Pubitemid 36539093)
15. H Cho JE Cronan 1993 Escherichia coli thioesterase I, molecular cloning and sequencing of the structural gene and identification as a periplasmic enzyme J Biol Chem 268 9238 9245 1:CAS:528:DyaK3sXkvFSjsr0%3D
16. M Choudhary X Zabhua YX Fu S Kaplan 2007 Genome analyses of three strains of Rhodobacter sphaeroides: evidence of rapid evolution of chromosome II J Bacteriol 189 1914 1921 1:CAS:528:DC%2BD2sXitl2hs7s%3D 10.1128/JB.01498-06 (Pubitemid 46446155)
17. GJM de Koning M Kellerhals C van Meurs B Witholt 1997 A process for the recovery of poly(hydroxyalkanoates) from Pseudomnas. Part 2: process, development and economic evaluation Bioprocess Eng 17 15 21 10.1007/ s004490050346 (Pubitemid 27298747)
18. JM Eraso S Kaplan 1994 prrA, a putative response regulator involved in oxygen regulation of photosynthesis gene expression in Rhodobacetr sphaeroides J Bacteriol 176 32 43 1:CAS:528:DyaK2cXht1Knu7Y%3D
19. Erb TJ (2009) The ethylmalonyl-CoA pathway: a novel acetyl-CoA assimilation strategy. Doctoral thesis, Albert-Ludwigs-Universität Freiburg
20. 2-units involving crotonyl-CoA carboxylase/reductase: the ethylmalonyl-CoA pathway Proc Natl Acad Sci USA 104 10631 10636 1:CAS:528:DC%2BD2sXnt1Ont74%3D 10.1073/pnas.0702791104 (Pubitemid 47185716)
21. 12- dependent acyl-CoA mutases J Biol Chem 283 32283 32293 1:CAS:528: DC%2BD1cXhtlOjtL%2FP 10.1074/jbc.M805527200
22. TJ Erb V Brecht G Fuchs M Müller BE Alber 2009 Carboxylation mechanism and stereochemistry of crotonyl-CoA carboxylase/reductase, a carboxylating enoyl-thioester reductase Proc Natl Acad Sci USA 106 8871 8876 1:CAS:528:DC%2BD1MXnsVant7k%3D 10.1073/pnas.0903939106
23. TJ Erb G Fuchs BE Alber 2009 (2S)-Methylsuccinyl-CoA dehydrogenase closes the ethylmalonyl-CoA pathway for acetyl-CoA assimilation Mol Microbiol 73 992 1008 1:CAS:528:DC%2BD1MXht1ajt7jE 10.1111/j.1365-2958.2009.06837.x
24. TJ Erb L Frerichs-Revermann G Fuchs BE Alber 2010 The apparent malate synthase activity of Rhodobacter sphaeroides is due to two paralogous enzymes, (3S)-malyl-coenzyme A (CoA)/β-methylmalyl-CoA lyase and (3S)-malyl-CoA thioesterase J Bacteriol 192 1249 1258 1:CAS:528:DC%2BC3cXivVSgu7s%3D 10.1128/JB.01267-09
25. AS Eustáquio RP McGlinchey Y Liu C Hazzard LL Beer G Florova MM Alhamadsheh A Lechner AJ Kale Y Kobayashi KA Reynolds BS Moore 2009 Biosynthesis of the salinosporamide A polyketide synthase substrate chloroethylmalonyl- coenzyme A from S-adenosyl-l-methionine Proc Natl Acad Sci USA 106 12295 12300 10.1073/pnas.0901237106
26. CB Fleck M Brock 2008 Characterization of an acyl-CoA:carboxylate CoA-transferase from Aspergillus nidulans involved in propionyl-CoA detoxification Mol Microbiol 68 642 656 1:CAS:528:DC%2BD1cXlsVOitL8%3D 10.1111/j.1365-2958.2008.06180.x (Pubitemid 351490186)
27. Fuchs G (1999) Biosynthesis of building blocks, chapter 7. In: Lengeler JW, Drews G, Schlegel HG (eds) Biology of the prokaryotes. Thieme, Stuttgart, pp 114-116
28. JL Gibson FR Tabita 1993 Nucleotide sequence and functional analysis of CbbR, a positive regulator of the Calvin cycle operons of Rhodobacter sphaeroides J Bacteriol 175 5778 5784 1:CAS:528:DyaK2cXhvFan
29. CW Goulding PM Bowers B Segelke T Lekin C-Y Kim TC Terwilliger D Eisenberg 2007 The structure and computational analysis of Mycobacterium tuberculosis protein CitE suggest a novel enzymatic function J Mol Biol 365 275 283 1:CAS:528:DC%2BD28Xht12ktLjK 10.1016/j.jmb.2006.09.086 (Pubitemid 44841972)
30. L Gu B Wang A Kulkarni TW Geders RV Gri L Gerwick K Håkansson P Wipf JL Smith WH Gerwick DH Sherman 2009 Metamorphic enzyme assembly in polyketide diversification Nature 459 731 735 1:CAS:528:DC%2BD1MXmvVWgtLY%3D 10.1038/nature07870
31. J Heider 2001 A new family of CoA-transferases FEBS Lett 509 345 349 1:CAS:528:DC%2BD3MXptFymtb8%3D 10.1016/S0014-5793(01)03178-7 (Pubitemid 34031958)
32. BR Howard JA Endrizzi SJ Remington 2000 Crystal structure of Escherichia coli malate synthase G complexed with magnesium and glyoxylate at 2.0∈Å resolution: mechanistic implications Biochemistry 39 3156 3168 1:CAS:528:DC%2BD3cXht1aitrg%3D 10.1021/bi992519h (Pubitemid 30159423)
33. AC Ind SL Porter MT Brown ED Byles JA de Beyer SA Godfrey JP Armitage 2009 Inducible-expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans Appl Environ Microbiol 75 6613 6615 1:CAS:528:DC%2BD1MXhtl2itLzJ 10.1128/AEM.01587-09
34. HM Joshi FR Tabita 1996 A global two component signal transduction system that integrates the control of photosynthesis, carbon dioxide assimilation, and nitrogen fixation Proc Natl Acad Sci USA 93 14515 14520 1:CAS:528: DyaK28XnsVKrsLw%3D 10.1073/pnas.93.25.14515 (Pubitemid 26418998)
35. FM Kapritchkoff AP Viotti RCP Alli M Zuccolo JGC Pradella AE Maiorano EA Miranda A Bonomi 2006 Enzymatic recovery and purification of ployhydroxybutyrate produced by Ralstonia eutropha J Biotechnol 122 453 462 1:CAS:528: DC%2BD28XjtFOms78%3D 10.1016/j.jbiotec.2005.09.009
36. BS Kim TA Cropp BJ Beck DH Sherman KA Reynolds 2002 Biochemical evidence for an editing role of thioesterase II in the biosynthesis of the polyketide pikromycin J Biol Chem 277 48028 48034 1:CAS:528:DC%2BD38Xptlehurc%3D 10.1074/jbc.M207770200 (Pubitemid 35470748)
37. A Koglin F Löhr F Bernhard VV Rogov DP Frueh ER Strieter MR Mofid P Güntert G Wagnaer CT Walsh MA Marahiel V Dötsch 2008 Structural basis for the selectivity of the external thioesterase of the surfactin synthetase Nature 454 907 911 1:CAS:528:DC%2BD1cXpvVaisbg%3D 10.1038/nature07161
38. 2-units by a modified tricarboxylic acid cycle Nature 179 988 991 1:CAS:528:DyaG2sXnslantQ%3D%3D 10.1038/179988a0
39. HL Kornberg PJR Phizackerley JR Sadler 1958 Synthesis of cell constituents from acetate by Escherichia coli Biochem J 72 32P 33P
40. 2 compounds in the methylotroph Methylobacterium extorquens AM1 J Bacteriol 183 1038 1046 1:CAS:528:DC%2BD3MXmsVOgsA%3D%3D 10.1128/JB.183.3.1038-1046.2001 (Pubitemid 32095314)
41. N Korotkova ME Lidstrom 2004 MeaB is a component of the methylmalonyl-CoA mutase complex required for protection of the enzyme from inactivation J Biol Chem 279 13652 13658 1:CAS:528:DC%2BD2cXis1elsrY%3D 10.1074/jbc.M312852200 (Pubitemid 38468893)
42. N Korotkova L Chistoserdova V Kuska ME Lidstrom 2002 Glyoxylate regeneration pathway in the methylotroph Methylobacterium extorquens AM1 J Bacteriol 184 1750 1758 1:CAS:528:DC%2BD38XitFSht7s%3D 10.1128/JB.184.6.1750- 1758.2002 (Pubitemid 34188227)
43. N Korotkova ME Lidstrom L Chistoserdova 2005 Identification of genes involved in the glyoxylate regeneration cycle in Methylobacterium extorquens AM1, including two genes, meaC and meaD J Bacteriol 187 1523 1526 1:CAS:528:DC%2BD2MXhs1Kktrs%3D 10.1128/JB.187.4.1523-1526.2005 (Pubitemid 40299478)
44. ME Kovach PH Elzer DS Hill GT Robertson MA Farris RM Roop KM Peterson 1995 Four derivatives of the braod-host range cloning vector pBBR1MCS carrying different antibiotic-resistance cassettes Gene 166 175 176 1:CAS:528: DyaK2MXps1WqtLw%3D 10.1016/0378-1119(95)00584-1
45. 1 compounds Biochem J 81 470 480 1:CAS:528:DyaF38Xislaiuw%3D%3D
46. RA Larsen MM Wilson AM Guss WW Metcalf 2002 Genetic analysis of pigmant biosynthesis in Xanthobacter autrophicus Py2 using a new, highly efficient transposon mutagenesis system that is functional in a wide variety of bacteria Arch Microbiol 178 193 201 1:CAS:528:DC%2BD38Xnt1egtbs%3D 10.1007/s00203-002- 0442-2 (Pubitemid 34985300)
47. J Li U Derewenda Z Dauetr S Smith ZS Derewenda 2000 Crystal structure of the Escherichia coli thioesterase II, a homolog of the human Nef binding enzyme Nat Struct Biol 7 555 559 1:CAS:528:DC%2BD3cXkslKntbk%3D 10.1038/76776 (Pubitemid 30445911)
48. S-K Lim SJ Kim SH Cha Y-K Oh H-J Rhee M-S Kim JK Lee 2009 Complete genome sequence of Rhodobacter sphaeroides KD131 J Bacteriol 191 1118 1119 1:CAS:528:DC%2BD1MXhtlGjtLg%3D 10.1128/JB.01565-08
49. CY Lin S Smith 1978 Properties of the thioesterase component obtained by limited trypsinization of the fatty acid synthetase multienzyme complex J Biol Chem 253 1954 1962 1:CAS:528:DyaE1cXhsVyjs7k%3D
50. Y Liu C Hazzard AS Eustáquio KA Reynolds BS Moore 2009 Biosynthesis of salinosporamides from α, β-unsaturated fatty acids: implications for extending polyketide synthase diversity J Am Chem Soc 131 10376 10377 1:CAS:528:DC%2BD1MXosVOgt7g%3D 10.1021/ja9042824
51. YC Lo SC Lin JF Shaw YC Liaw 2003 Crystal structure of Escherichia coli thioesterase I/protease I/lysophospholipase L1: consensus sequence blocks constitute the catalytic center of SGNH-hydrolases through a conserved hydrogen bond network J Mol Biol 330 539 551 1:CAS:528:DC%2BD3sXkvFGgsbc%3D 10.1016/S0022-2836(03)00637-5 (Pubitemid 36808687)
52. Marx A, Poetter M, Buchholz S, May A, Siegert H, Alber B, Fuchs G, Eggerling L (2007) Microbiological production of 3-hydroxybutyric acid. WO/2007/141208
53. M Meister S Saum BE Alber G Fuchs 2005 L-Malyl-coenzyme A/β-methylmalyl-coenzyme A lyase is involved in acetate assimilation of the isocitrate lyase-negative bacterium Rhodobacter capsulatus J Bacteriol 187 1415 1425 1:CAS:528:DC%2BD2MXhs1Kksbw%3D 10.1128/JB.187.4.1415-1425.2005 (Pubitemid 40299466)
54. Neidhardt FC, Ingraham JL, Schaechter M (1990) In: Physiology of the bacterial cell. Chapter 5: biosynthesis and fueling. Sinauer, Sunderland, pp 133-172
55. 13C metabolomics Proc Nat Acad Sci USA 106 4846 4851 1:CAS:528:DC%2BD1MXktFGqtbk%3D 10.1073/pnas.0810932106
56. CM Pickart WP Jencks 1979 Formation of stable anhydrides from CoA transferase and hydroxamic acids J Biol Chem 254 9120 9129 1:CAS:528: DyaE1MXlvVyltrs%3D
57. J Quandt MF Hynes 1993 Versatile suicide vectors which allow direct selection for gene replacement in Gram-negative bacteria Gene 127 15 21 1:CAS:528:DyaK3sXktVWqtbo%3D 10.1016/0378-1119(93)90611-6 (Pubitemid 23140440)
58. J Rétey 1990 Enzymatic reaction selectively by negative catalysis or how do enzymes deal with highly reactive intermediates Angew Chem Int Ed 29 355 361 10.1002/anie.199003551 (Pubitemid 20155149)
59. JH Roh WE Smith S Kaplan 2004 Effects of oxygen and light intensity on transcriptome expression in Rhodobacter sphaeroides 2.4.1. Redox active gene epression profile J Biol Chem 279 9146 9155 1:CAS:528:DC%2BD2cXhs1Oms78%3D 10.1074/jbc.M311608200 (Pubitemid 38295978)
60. T Rohwerder RH Müller 2010 Biosynthesis of 2-hydroxyisobutyric acid (2-HIBA) from renewable carbon Microb Cell Fact 25 13 10.1186/1475-2859-9-13
61. A Schäfer A Tauch W Jager J Kalinowski G Thierbach A Puhler 1994 Small mobilizable multipurpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum Gene 145 69 73 10.1016/0378-1119(94)90324-7 (Pubitemid 24224965)
62. J Schrader M Schilling D Holtmann D Sell MV Filho A Marx JA Vorholt 2008 Methanol-based industrial biotechnology: current status and future perspectives of methylotrophic bacteria Trends Biotechnol 27 107 115 10.1016/j.tibtech.2008. 10.009
63. D Schwarzer HD Mootz U Linne MA Marahiel 2002 Regeneration of misprimed nonribosomal peptide synthases by type II thioesterases Proc Natl Acad Sci USA 99 14083 14088 1:CAS:528:DC%2BD38XosF2itrg%3D 10.1073/pnas.212382199 (Pubitemid 35257628)
64. MW Sganga CE Bauer 1992 Regulatory factors controlling photosynthetic reaction center and light-harvesting gene expression in Rhodobacter capsulatus Cell 68 945 954 1:CAS:528:DyaK3sXhvVCqtL4%3D 10.1016/0092-8674(92)90037-D
65. LM Smith WG Meijer L Dijkuizen PM Goodwin 1996 A protein having similarity with methylmalonyl-CoA mutase is required for the assimilation of methanol and ethanol by Methylobacterium extorquens AM1 Microbiology 142 675 684 1:CAS:528:DyaK28XhvVSntro%3D 10.1099/13500872-142-3-675
66. JB Thoden HM Holden Z Zhuang D Dunaway-Mariano 2002 X-ray crystallographic analyses of inhibitor and substrate complexes of wild-type and mutant 4-hydroxybenzoyl-CoA thioesterase J Biol Chem 277 27468 27476 1:CAS:528:DC%2BD38XlvV2iu7k%3D 10.1074/jbc.M203904200 (Pubitemid 34951767)
67. JB Thoden Z Zhuang D Dunaway-Mariano HM Holden 2003 The structure of 4-hydroxybenzoyl-CoA thioesterase from Arthrobacter sp. strain SU J Biol Chem 278 43709 43716 1:CAS:528:DC%2BD3sXosFSrtrg%3D 10.1074/jbc.M308198200 (Pubitemid 37345998)
68. MD Vlasie R Banerjee 2004 When a spectator turns killer: suicidal electron transfer from cobalamin in methylmalonyl-CoA mutase Biochemistry 43 8410 8417 1:CAS:528:DC%2BD2cXksF2hsbc%3D 10.1021/bi036299q (Pubitemid 38902519)
69. 2 fixation in Rhodobacter sphaeroides and evidence that ribulose bisphosphate carboxylase/oxygenase activity serves to maintain the redox balance of the cell J Bacteriol 175 3372 3379 1:CAS:528:DyaK3sXkvFSqtb0%3D
70. J Zarzycki A Schlichting N Strychalsky M Müller BE Alber G Fuchs 2008 Mesaconyl-coenzyme A hydratase, a new enzyme of two central carbon metabolic pathways in bacteria J Bacteriol 190 1366 1374 1:CAS:528: DC%2BD1cXhvVOls7Y%3D 10.1128/JB.01621-07 (Pubitemid 351215019)
71. Z Zhuang K-H Gartemann R Eichnelaub Dunaway-Mariano 2003 Characterization of the 4-hydroxybenzoyl-coenzyme A tioesterase from Arthrobacter sp. strain SU Appl Environ Microbiol 69 2707 2711 10.1128/AEM.69.5.2707-2711.2003 (Pubitemid 36560348)